Fixed generic compile.

src/dp/swipe/banded_3frame_swipe.cpp

@@ -531,18 +531,18 @@ void banded_3frame_swipe_worker(vector<DpTarget>::const_iterator begin,
 #ifdef __SSE2__
 		out->splice(out->end(), banded_3frame_swipe_targets<score_vector<int16_t>>(begin + pos, min(begin + pos + config.swipe_chunk_size, end), score_only, *query, strand, stat, true, of));
 #else
-		out->splice(out->end(), banded_3frame_swipe_targets<int32_t>(begin + pos, min(begin + pos + config.swipe_chunk_size, end), score_only, *query, strand, stat, true, false, of));
+		out->splice(out->end(), banded_3frame_swipe_targets<int32_t>(begin + pos, min(begin + pos + config.swipe_chunk_size, end), score_only, *query, strand, stat, true, of));
 #endif
 	*overflow = std::move(of);
 }
 
 list<Hsp> banded_3frame_swipe(const TranslatedSequence &query, Strand strand, vector<DpTarget>::iterator target_begin, vector<DpTarget>::iterator target_end, DpStat &stat, bool score_only, bool parallel)
 {
+	vector<DpTarget> overflow16, overflow32;
 #ifdef __SSE2__
 	task_timer timer("Banded 3frame swipe (sort)", parallel ? 3 : UINT_MAX);
 	std::stable_sort(target_begin, target_end);
 	list<Hsp> out;
-	vector<DpTarget> overflow16, overflow32;
 	if (parallel) {
 		timer.go("Banded 3frame swipe (run)");
 		vector<thread> threads;
@@ -576,11 +576,10 @@ list<Hsp> banded_3frame_swipe(const TranslatedSequence &query, Strand strand, ve
 		out = banded_3frame_swipe_targets<score_vector<int16_t>>(target_begin, target_end, score_only, query, strand, stat, false, overflow16);
 
 	out.splice(out.end(), banded_3frame_swipe_targets<int32_t>(overflow16.begin(), overflow16.end(), score_only, query, strand, stat, false, overflow32));
+	return out;
 #else
-	out = banded_3frame_swipe_targets<int32_t>(target_begin, target_end, score_only, query, strand, stat, false, overflow);
+	return banded_3frame_swipe_targets<int32_t>(target_begin, target_end, score_only, query, strand, stat, false, overflow32);
 #endif
-
-	return out;
 }
 
 }

src/dp/swipe/banded_swipe.cpp

@@ -377,7 +377,9 @@ void swipe(const sequence &query, Frame frame, vector<DpTarget>::const_iterator
 	}
 }
 
+#ifdef __SSE2__
 template void swipe<score_vector<int16_t>, Traceback>(const sequence&, Frame, vector<DpTarget>::const_iterator, vector<DpTarget>::const_iterator);
 template void swipe<score_vector<int16_t>, ScoreOnly>(const sequence&, Frame, vector<DpTarget>::const_iterator, vector<DpTarget>::const_iterator);
+#endif
 
 }}}

src/dp/swipe/swipe.cpp

@@ -160,6 +160,8 @@ vector<int> swipe(const sequence &query, const sequence *subject_begin, const se
 {
 #ifdef __SSE2__
 	return swipe<score_vector<uint8_t>>(query, subject_begin, subject_end);
+#else
+	return {};
 #endif
 }
 

src/tools/benchmark.cpp

@@ -73,6 +73,7 @@ void benchmark_ungapped(const sequence &s1, const sequence &s2)
 	cout << "Scalar ungapped extension:\t" << (double)time_span.count() / (n*40) * 1000 << " ps/Cell" << endl;
 }
 
+#ifdef __SSSE3__
 void benchmark_ungapped_sse(const sequence &s1, const sequence &s2)
 {
 	static const size_t n = 100000000llu;
@@ -89,6 +90,7 @@ void benchmark_ungapped_sse(const sequence &s1, const sequence &s2)
 	}
 	cout << "SSE score shuffle:\t\t" << (double)duration_cast<std::chrono::nanoseconds>(high_resolution_clock::now() - t1).count() / (n * 16) * 1000 << " ps/Letter" << endl;
 }
+#endif
 
 void benchmark_transpose() {
 	static const size_t n = 100000000llu;
@@ -102,6 +104,7 @@ void benchmark_transpose() {
 	cout << "Matrix transpose 16x16 bytes:\t" << (double)duration_cast<std::chrono::nanoseconds>(high_resolution_clock::now() - t1).count() / (n * 256) * 1000 << " ps/Letter" << endl;
 }
 
+#ifdef __SSE2__
 void swipe_cell_update() {
 	static const size_t n = 1000000000llu;
 	high_resolution_clock::time_point t1 = high_resolution_clock::now();
@@ -122,6 +125,7 @@ void swipe_cell_update() {
 	}
 	cout << "SWIPE cell update (int8_t):\t" << (double)duration_cast<std::chrono::nanoseconds>(high_resolution_clock::now() - t1).count() / (n * 16) * 1000 << " ps/Cell" << endl;
 }
+#endif
 
 void swipe(const sequence &s1, const sequence &s2) {
 	sequence target[16];
@@ -153,11 +157,15 @@ void benchmark() {
 	s2 = sequence::from_string("erlvelvtmmgdqgelpiamalanvvpcsqwdelarvlvtlfdsrhllyqllwnmfskeveladsmqtlfrgnslaskimtfcfkvygatylqklldpllrivitssdwqhvsfevdptrlepsesleenqrnllqmtekffhaiissssefppqlrsvchclyqvvsqrfpqnsigavgsamflrfinpaivspyeagildkkpppiierglklmskilqsianhvlftkeehmrpfndfvksnfdaarrffldiasdcptsdavnhslsfisdgnvlalhrllwnnqekigqylssnrdhkavgrrpfdkmatllaylgppe");
 
 	benchmark_ungapped(s1, s2);
+#ifdef __SSSE3__
 	benchmark_ungapped_sse(s1, s2);
+#endif
 	benchmark_transpose();
-	swipe_cell_update();
+#ifdef __SSE2__
 	swipe(s1, s2);
 	banded_swipe(s1, s2);
+	swipe_cell_update();
+#endif
 }
 
 }}

src/util/simd.h

@@ -52,7 +52,6 @@ namespace SIMD {
 enum class Arch { None, Generic, SSE4_1 };
 enum Flags { SSSE3 = 1, POPCNT = 2, SSE4_1 = 4 };
 Arch arch();
-extern int flags;
 
 #define DECL_DISPATCH(ret, name, param) namespace ARCH_GENERIC { ret name param; }\
 namespace ARCH_SSE4_1 { ret name param; }\